Healthy Pumpkin Muffins

Healthy Pumpkin Muffins are soft, moist, easy to make, and loaded with wholesome ingredients including whole wheat flour and yogurt…but they’re so yummy that nobody will ever guess they’re healthy!

Healthy Pumpkin Muffins on plate and cooling rack.

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Pumpkin season has arrived, friends! Each fall, I look forward to developing at least a couple new pumpkin recipes. I already have a scrumptious pumpkin muffin recipe in the ol' archive, but since it's of the decadent, sugar-loaded variety, I typically only make it once per year. However, I've always wanted a more wholesome pumpkin muffin recipe to feel good about making throughout the season, and I'm so pleased with how these Healthy Pumpkin Muffins turned out!

Healthy Pumpkin Muffins lined up on rack.

I tweaked my beloved Healthy Banana Muffins recipe for this pumpkin version, and the final result did not disappoint. These Healthy Pumpkin Muffins are soft, light, airy, and perfectly spiced. And everyone who tastes them will be shocked to learn that they're 100% whole wheat! You're going to LOVE them.

Ingredients

The ingredients are simple and wholesome.

Labeled ingredients to make Healthy Pumpkin Muffins.
  • Whole wheat pastry flour. This is the key, y'all! Whole wheat pastry flour is 100% whole wheat, but it yields a lighter taste and texture than regular whole wheat flour, making it more akin to the results you'd get from all-purpose flour when it comes to baking muffins, cookies, cakes, etc. But that doesn't change the fact that it boasts the nutrition of regular whole wheat flour! That being said, if you'd like to use regular all-purpose flour instead in this recipe, it will work great.
  • Pumpkin pie spice. I always keep a jar of Homemade Pumpkin Pie Spice in the pantry for all of my favorite fall goodies. But if you don't have any on hand, you can always substitute 2 teaspoons cinnamon, ½ teaspoon ginger, ½ teaspoon nutmeg, ¼ teaspoon allspice, and a pinch of ground cloves in its place.
  • Baking powder, baking soda, and salt. Make sure your baking powder and soda are fresh so that your muffins rise. And I'm never without my favorite salt!
  • Pumpkin puree. This recipe uses one whole can of store-bought pumpkin puree...just make sure you don't buy pumpkin pie filling by mistake (which has sugar and other ingredients added)! Or, if you're feeling extra-ambitious, you can use about 1 ⅔ cups of Homemade Pumpkin Puree.
  • Pure maple syrup. I love the warm flavor this natural sweetener lends these Healthy Pumpkin Muffins. But you can opt to swap for honey, if you wish.
  • Coconut oil. Melted and slightly cooled. Any neutral-flavored oil may be substituted for the coconut oil. I sometimes make this recipe with avocado oil instead.
  • Eggs. At room temperature.
  • Pure vanilla extract. Always use the real stuff!
  • Plain yogurt. At room temperature. You can use regular yogurt or Greek yogurt...either way, it will add extra moisture to your muffins.
Aerial view of Healthy Pumpkin Muffins.

How to Make Healthy Pumpkin Muffins

(The below photos are intended to be helpful, but please refer to the recipe card at the bottom of this post for FULL DIRECTIONS.)

This pumpkin muffin recipe is easy-peasy! You can mix up the batter by hand...no need for an electric mixer.

  1. Preheat the oven to 350°F. Prepare two pans by lining 24 muffin cups with paper liners.
Cupcake liners in muffin pans.
  1. In a medium bowl, whisk together the flour, pumpkin pie spice, baking powder, baking soda, and salt.
Dry ingredients in bowl for Healthy Pumpkin Muffins recipe.
Dry ingredients whisked together.
  1. In a large bowl, mix together the pumpkin puree, maple syrup, coconut oil, eggs, and vanilla until well combined.
Pumpkin, maple syrup, coconut oil, eggs, and vanilla in bowl.
Wet ingredients for Healthy Pumpkin Muffins combined in bowl.
  1. Add half of the flour mixture and stir to combine.
Adding flour to batter.
Flour mixed into batter for Healthy Pumpkin Muffins recipe.
  1. Stir in the yogurt.
Adding yogurt to bowl.
Yogurt blended into Healthy Pumpkin Muffins batter.
  1. Add the remaining flour mixture and stir until just blended.
Adding remaining flour to Healthy Pumpkin Muffins recipe.
Batter ready for easy pumpkin muffins.
  1. Divide the batter between the prepared muffin pans, filling each muffin cup about ⅔ full with batter (I like to use a big cookie scoop to make this step neater and easier).
Pumpkin muffin recipe ready for the oven.
  1. Bake for 15 to 17 minutes, or until a toothpick inserted in the center of a muffin comes out clean.
Healthy Pumpkin Muffins fresh out of the oven.
  1. Cool your Healthy Pumpkin Muffins in the pans for about five minutes before turning them out onto wire racks to finish cooling completely.
Healthy Pumpkin Muffins on cooling rack.

Optional Add-Ins or Toppings

I find these Healthy Pumpkin Muffins to be perfectly delightful as-is. But if you'd like to embellish them with additional ingredients (stirred into the batter or sprinkled on top), be my guest! 🙂

A few suggestions to jazz up your easy pumpkin muffins:

  • Chopped nuts, such as pecans or walnuts. For extra crunch, I recommend toasting nuts before stirring them into the batter.
  • Chocolate chips. Regular or mini.
  • Raisins or dried cranberries.
  • Coarse sugar sprinkled on top, such as sparkling sugar or turbinado sugar.
  • Streusel topping (an idea borrowed from my Healthy Whole Wheat & Honey Applesauce Muffins). Simply combine ⅔ cup brown sugar1 cup rolled oats, and 1 teaspoon cinnamon in a small bowl. Using a fork or your fingers, work in 4 tablespoons softened butter (I prefer salted, but unsalted will work) until crumbly. Sprinkle over the tops of the muffins before baking as directed.
Healthy Pumpkin Muffins on platter with more muffin in background.

If you haven't already launched into your fall baking, I hope these Healthy Pumpkin Muffins inspire you! They're healthy enough for breakfast, make a great portable snack, and are tasty enough for dessert.

Happy fall, y'all!

Close-up of pumpkin muffin recipe with missing bite.

More Pumpkin Recipes

Healthy Pumpkin Muffins in rows on cooling rack.

Healthy Pumpkin Muffins

Healthy Pumpkin Muffins are soft, moist, easy to make, and loaded with wholesome ingredients including whole wheat flour and yogurt…but they’re so yummy that nobody will ever guess they’re healthy!
Course: Quick Bread & Muffins
Cuisine: American
Prep Time: 15 minutes
Cook Time: 15 minutes
Total Time: 30 minutes
Servings: 24 muffins
Calories: 134kcal
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Ingredients

  • 2 ½ cups whole wheat pastry flour
  • 1 tbsp pumpkin pie spice, heaping
  • 1 ½ teaspoons baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 1 (15-ounce) can pumpkin puree
  • 1 cup maple syrup
  • ½ cup coconut oil, melted and slightly cooled
  • 2 eggs, at room temperature
  • 2 teaspoons vanilla
  • cup yogurt, at room temperature

Instructions

  • Preheat oven to 350°F. Prepare muffin pans by lining 24 muffin cups with nonstick paper cupcake liners.
  • In a medium bowl, whisk together flour, pumpkin pie spice, baking powder, baking soda, and salt. In a large bowl, mix together pumpkin puree, maple syrup, coconut oil, eggs, and vanilla. Add half of flour mixture; stir. Add yogurt; stir. Add remaining flour mixture; stir until just blended.
  • Divide batter between muffin pans by filling each muffin cup approximately ⅔ full with batter. Bake for 15 to 17 minutes or until toothpick inserted in center of muffin comes out clean. Cool in pans for a few minutes before turning out onto wire rack to cool completely.

Notes

  • If you don’t have any Pumpkin Pie Spice on hand, you can substitute 2 teaspoons cinnamon, ½ teaspoon ground nutmeg, ½ teaspoon ground ginger, ¼ teaspoon allspice, and a pinch of ground cloves. Or if you are missing any of those spices, just increase the cinnamon by an equivalent amount.
  • Make sure your ingredients are at room temperature or else your melted coconut oil will resolidify as soon as the cold ingredients touch it. You can quickly warm up cold eggs by putting them in a bowl of warm water for a few minutes.
  • All-purpose white flour may be substituted for the whole wheat pastry flour, if you wish.
  • Honey may be substituted for the maple syrup.
  • Any neutral-flavored oil may be substituted for the coconut oil. I sometimes make these muffins with avocado oil instead.

Nutrition

Calories: 134kcal | Carbohydrates: 20g | Protein: 3g | Fat: 5g | Saturated Fat: 4g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 1g | Trans Fat: 0.001g | Cholesterol: 15mg | Sodium: 105mg | Potassium: 155mg | Fiber: 2g | Sugar: 9g | Vitamin A: 2786IU | Vitamin C: 1mg | Calcium: 46mg | Iron: 1mg
Made this recipe? I'd love to see on IG!Mention @FiveHeartHome or tag #FiveHeartHome!

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5 from 2 votes

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4 Comments

    1. Makes me so happy to hear that, Chynna! My family loves them, too...I've already had to make them twice in under a week -- ha. 😉